21 September, 2008

Upcoming training events October

As usual October is a busy month for the Ensembl trainers with workshops on 4(!) different continents.

From 1-3 Oct Ensembl will feature in the Wellcome Trust Open Door Workshop "Working with the Human Genome Sequence" in Hyderabad, India, and from 6-8 Oct in the EBI hands-on workshop "A two-day dip into the EBI’s data resources: Understanding your data" in Hinxton, UK.

Upcoming browser workshops:
9-10 Oct: J. Craig Venter Institute, Rockville, MD, US
14 Oct: National Human Genome Research Institute (NHGRI), Bethesda, MD, US
15 Oct: National Human Genome Research Institute (NHGRI), Bethesda, MD, US
16-17 Oct: University of the Free State, Bloemfontein, South Africa
20-21 Oct: University of the Witwatersrand, Johannesburg, South Africa
22 Oct: University of Nottingham, Nottingham, UK
23-24 Oct: University of the Western Cape, Cape Town, South Africa
29-30 Oct: EBI Roadshow, Dublin, Ireland

If you want to know to which locations we are coming after October, then have a look at the complete list of all upcoming training events.

Considering hosting an Ensembl workshop yourself? Please contact Xose Fernandez.

18 September, 2008

Websites and Guinness. Worth the wait.

Steve posted the news that we're delaying our new release for at least two more weeks. The message is pasted in here:

Hi all

In our Intentions Summary mail for release 51 we stated that the release was scheduled for early/mid September. The 51 release will include significant updates and improvements to the web interface. We are delaying release while we complete development on these. We are working to get the release out as soon as possible, and are now aiming for end September/early October. I apologise for this delay.


Dr Steve Searle
Ensembl Project Leader, Sanger

It is always so frustrating to delay, but of course, far more important to have a working site than something only part working. Welcome to delivering high end services.

We took on alot of things to change in this web refresh. For most users the main thing people will notice is the entirely new web layout. This was driven by our surveys of users who mainly complained about being buried in too many displays and data. We then took around 4 months working with user groups and trialling different layouts (many thanks for those who participated) which in some cases made significant changes to our original designs (we now have a hybrid "tab and left-hand-side" approach, voted as best by ~60% of people, with the other three options splitting the rest of vote). We're very excited about this new layout going live as it just looks cleaner, less cluttered and yet providing more information. The other thing people will notice is that it is just faster. As the saying goes, you can't be too rich, too thin or have your websites go too fast.

Making a website go faster is harder than it might look. It involves all sorts of things - the bandwidth of your machines to us, the speed the servers, the connectivity of servers to databases, the speed of the API, the database to disk, the management of the huge number of simultaneous users we have and then the size of the html returned and finally the render speed on your browser. All of these contribute to the overall perception of "speed". Under the hood we've been working on all these aspects - internally a big change is that we have switched from needing a common file system for our web farm to work off. Previously when your browser asks for a contigview page, our servers generates html with an image and that image is written to the common disk, the browser parses the image tag, asks for this image - and this is the critical bit - sends a request which in all likelihood will be served by a different server in our webfarm. That server then went to the common file system to pick up the file and send it back. Many times a critical bottleneck has been read/write on this shared filesystem. In the new system this has all gone, and the images are stored in a memory-based common store, meaning both that we remove this bottle-neck (which will be the first big effect) and secondly we will be able to cache alot more - the hope is that many of the identical pictures for the common species will be entirely served from memory in the new system. Another important change has been aggressively sliming our html. Currently all sorts of files - often very small - are pinged by each page up, just to see if they have changed. We've consolidated alot of these files - and compressed them - and then also optimised them for render speed.

There is a variety of things not for this release but coming up end of 2008/early 2009 also on speed. Our API has a new concept, collections, which better handles the case of zoomed out views, where we know the renders will not be able to render every object. Instead a collection - which may be rendered as a union or density or something will be provided. The other thing on the horizon is us setting up a US mirror on the west coast. For the last year we have been extensively monitoring the speed of Ensembl from different sites, and there is a large increase in time to retrieve on the north-west coast of the US. We've been investigating quite why this (and learning lots more about the backbone of the internet than we knew before) but it seems as if the simplest way to getting speed to work in the west coast is to just run a mirror over there. Probably 2009 for that to go live.

Back to the website. It looks so much better - and has much better hardware characteristics - (our shared file system is ... well ... rather 2004 technology and needs pretty constant care at the moment) that I can't wait until it comes out. But there is absolutely no point in having a crippled site in functionality even though we've got many of the user interface and technical issues right. The sticking point at the moment is the configuration panel. This comes up as "modal" box on top of the page, allowing alot of options to choose from, but not a bewildering set of options on each page. To cope with the 200 odd different tracks to switch on and off, the box has to have tabs and friendly, browseable hieriarchies. To get all this to work in a nice, friendly, slick way... that's alot of Javascript.

And alot of Javascript is alot of browser compatible headaches. Even using JS libraries - prototype and scriptolicious (I think - James smith can tell you the details!) there are all sorts of details that might not work just-quite the same way on IE5 compared to IE6. Or Firefox. Or Safari. And it must degrade at least functionally without JS. And of course work, and render fast. This modal box is the last, complex thing to get sorted.

We're close. I've seen the box come up over James' screen. I hear Steve has seen it come and tracks change, and see the link of tracks to changes. The API for the configuration system was gutted and is much better. But its got to work on all main browsers. For all our genomes, in particular Human and Mouse. And this is just tricky, fiddly work.

We're not quite there yet. We're really close, and so much is working it is just excruitiating. But we need another couple of weeks. James is being shielded from other jobs by Steve and others; Eugene is torture testing memcachedb to stress test the system before it goes live; Xose, Bert and Guilietta are writing help; Beth and Anne are writing the additional pagelets inside of the new geneview and transcriptviews. and it all looks really good.

So - apologies - we thought we'd be launching in July. We thought we'd be launching in September. We still might just do that, but then again, it might well be October. If it goes any later I will have no hair.

But it does look really good.

It is definitely worth the wait. Like Guinness.